LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses.

Autor: Drummond AJ; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; School of Biological Sciences, University of Auckland, Auckland, New Zealand.; School of Computer Science, University of Auckland, Auckland, New Zealand., Chen K; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; School of Biological Sciences, University of Auckland, Auckland, New Zealand.; School of Computer Science, University of Auckland, Auckland, New Zealand., Mendes FK; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; Department of Biology, Washington University in St. Louis, St. Louis, United States of America., Xie D; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; School of Biological Sciences, University of Auckland, Auckland, New Zealand.; School of Computer Science, University of Auckland, Auckland, New Zealand.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2023 Jul 18; Vol. 19 (7), pp. e1011226. Date of Electronic Publication: 2023 Jul 18 (Print Publication: 2023).
DOI: 10.1371/journal.pcbi.1011226
Abstrakt: Phylogenetic models have become increasingly complex, and phylogenetic data sets have expanded in both size and richness. However, current inference tools lack a model specification language that can concisely describe a complete phylogenetic analysis while remaining independent of implementation details. We introduce a new lightweight and concise model specification language, 'LPhy', which is designed to be both human and machine-readable. A graphical user interface accompanies 'LPhy', allowing users to build models, simulate data, and create natural language narratives describing the models. These narratives can serve as the foundation for manuscript method sections. Additionally, we present a command-line interface for converting LPhy-specified models into analysis specification files (in XML format) compatible with the BEAST2 software platform. Collectively, these tools aim to enhance the clarity of descriptions and reporting of probabilistic models in phylogenetic studies, ultimately promoting reproducibility of results.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
Databáze: MEDLINE
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